A ferredoxin-like domain in RNA polymerase 30/40-kDa subunits

Abstract

The 30/40-kDa subunits of DNA-dependent RNA polymerases (EC 2.7.7.6) form a protein family named RPB3/RPC5, with members in animals[1], plants[2], yeasts[3], protozoa[4]and archaea[5, 6]. These subunits are essential components of the transcription apparatus in eukaryotes[7]and are also remotely similar to the RpoA bacterial DNA-dependent RNA polymerases (α chain)[6]. The RPB3 subfamily members are subunits of RNA polymerase II (Ref. [7]), while the RPC5 subfamily members are subunits of RNA polymerases I and III (Ref. [3]). With the complete sequencing of the Methanococcus jannaschii genome[8], the RpoD protein (ORF MJ0192) has been found to be highly similar to the RpoD protein from Sulfolobus acidocaldarius[9, 10], a member of this family. However, while the M. jannaschii protein identifies all members of the family with BLAST[11]scores of more than 132 and p-values less than 1.4e-11 in the non-redundant protein database, the S. acidocaldarius protein[6](herein called aRpoD—to distinguish it from the RpoD sigma subunit) in addition identifies ferredoxin domains with scores as high as 120 and p-values as low as 1.2e-09, which have not been recognized before[6].